Lack of defense systems drives Enterococcus easily evolved into lysogens

Abstract Background: Enterococcus are important opportunistic pathogens that readily acquire foreign genes and could be easily lysogenized by phages. But no comparative genomic analysis of Enterococcus prophages had been undertaken to date. The prophage distribution, potential contribution and the relationship with Enterococcus defensive system remain unclear. Result: This study presents a comparative analysis of 563 putative prophages identified in 107 chromosomes and 301 plasmids of Enterococcus. Our result suggested that lysogens are highly prevalent in Enterococcus and Enterococcus genomes have more prophages than other bacteria, the number of prophages are related with strains pathogenicity, groups and isolated regions, and the prophages distribution present phylogeographic pattern. By analyzing the prophages characteristic, it is found that prophages can be divided into many clusters, but most of prophages have distant genetic relationship with sequenced phages and remain unreported; Prophages integrated into chromosomes and plasmids have different evolutionary origins, and show different genomes size, GC% and genes characteristic. It should be noted that all antibiotic resistance genes are carried by plasmids prophages and E. faecium plasmid prophages play important roles in transmission of vancomycin resistance genes through plasmid conjugation transfer and phages transduction. By investigating and statistical analyzing the relationship between major defend systems and the number of prophages, it indicated that R-M system often absent in Enterococcus, orphan CRISPR array prevalent in most of Enterococcus, and the presence of CRISPR-spacers and the absence of prophages in lysogen is inversely related. Conclusion: To our knowledge, this is the first systematic analysis of Enterococcus prophages distribution, potential contribution and phylogeny, and elucidate the relationship between defense system and lysogeny in Enterococcus. This information helps to understand how prophages affect its hosts diversity, fitness and evolution.